Moving to my own space

I’ve just registered a new domain — gravitropic.net — where I will continue what I started here. I’ve moved a few of the more recent posts over there from here, but will leave the rest here at WordPress.

Edward Tufte’s “Slopegraphs”

Edward Tufte’s “Slopegraphs”. I’ve been toying with the idea of employing a plot like this in a manuscript I’m working on, but I’m concerned about how it will be received.

College grade inflation

Several eye-popping observations in this piece on college grade inflation from the NY Times. Here’s one of the money quotes:

They then attribute the rapid rise in grade inflation in the last couple of decades to a more “consumer-based approach” to education, which they say “has created both external and internal incentives for the faculty to grade more generously.” More generous grading can produce better instructor reviews, for example, and can help students be more competitive candidates for graduate schools and the job market.

The potato genome is solved

The potato genome sequence is reported in this week’s Nature, through the collaborative efforts of 26 research institutes around the world. Like many plants, potato has a polyploid genome, making the assembly of sequence data a challenge. In the case of potato, there are 4 versions of each chromosome, each of which tends to show high diversity, known as heterozygosity. Because all of our commercial potato cultivars are clones, they remain highly vulnerable to disease, so having an entire reference sequence to identify new potential resistance genes from wild relatives will be a real help to breed more resistance traits.

In Louisiana, a Small College Gives Itself a Makeover

Massive overhaul of the curriculum at Centenary:

It also proposed that Centenary redefine itself by focusing programs on giving students both the capacity to meet the challenges of the 21st century and opportunities for hands-on engagement with issues.

I guess the question is whether the faculty, or anyone else, can identify with any certainty and in advance what the challenges of the 21st century will be. It was always my understanding that the strength of a liberal arts education lies in its flexibility.

Online courses in strange places

There’s an interesting piece on the Wired Campus blog about teaching online courses at liberal arts colleges. I think the most interesting observation was near the end of the post:

Just how professors could make use of time in their classes, if the computer took over some of the basics, was something that everyone wondered. And nobody had good answers. “We’re in uncharted territory here,” said Ms. Cassidy.

The fact of the matter is that most of us don’t know what a college classroom looks like without lecture — it’s what we grew up with, and what we expect to be doing. Anything else tends to feel like I’m not quite fulfilling my obligation to the students, and they tend to feel the same. I’ve followed with interest the posts over on Casting Out Nines about the inverted classroom, and I sometimes let my mind wander to what such an inversion may look like in my classes. I read a description of the wholesale re-imagining of physics instruction and feel inspired, but overwhelmed.

Installing a system of online content and exposing students to the basic facts before showing up for class is without a doubt essential, but it’s only a first step, as the Wired Campus post indicates. What happens after that is where the innovation needs to happen. In a recent article in Science, a group of science educators, including the author of a leading introductory biology text, reported on their success in employing more active learning in their intro biology course, including what the authors describe as much more practice with the information. Producing a class with the right kinds of practice problems and group exercises seems to be where the magic lies, as the study authors indicate themselves.

Complexities of organic vs sustainable

A thoughtful piece on the complex issues surrounding organic-certified crops and farming practices that may be more sustainable even though not “organic”:

Conventional farmers of herbicide-tolerant corn and soybean, are able to use low-till and no-till agriculture, which leaves the topsoil intact and protects it from being removed by wind or rain. Such no-till methods improve water quality and reduce soil erosion. Also, because tractor tilling is minimized, less fuel is consumed and greenhouse gas emissions are reduced.

via Is Organic Food the Answer? : Tomorrow’s Table.

Lack of Sex Among Wine Grapes Saps Its Genetic Health – NYTimes.com

Looks like wine grape varieties are more closely related than previously thought:

Much to his surprise he found that 75 percent of the varieties were as closely related as parent and child or brother and sister. “Previously people thought there were several different families of grape,” Dr. Myles said. “Now we’ve found that all those families are interconnected and in essence there’s just one large family.”

via Lack of Sex Among Wine Grapes Saps Its Genetic Health – NYTimes.com.

An iPad for the lab and beyond

The Idea

In my lab, almost everything we do ends up in digital form of some sort or another: data collected by the image analysis software as CSV files, confocal scans as TIFF files, gels as JPG files, etc. So a few years ago, I installed MediaWiki on the lab server to serve as an online lab notebook. It was great, I posted PDFs there for students to read as background, and lab protocols, and students even maintained their own lab notebook pages. Then the server died, and because I’m not full-time tech support, we quit using it. Then OWU subscribed to Wikispaces, and we’re back in business with a vibrant, active wiki that (hopefully) captures most of what we’re working on in the lab.

One thing I’ve noticed over the last two years is that students will work somewhere in the lab or down on the microscope, take notes on scrap paper, and eventually enter their notes on a particular trial or experiment on the wiki (or not). So when the iPad came out, I started to wonder how good it would be as a readily available (instant-on) bench computer. Two weeks ago, I started testing one in the lab, with the idea that if it works well, maybe I’ll try to put together a workflow for using them in an upper-level teaching lab.

First test case – confocal microscope data

My first chance to use the iPad in the lab presented itself last week, when I was imaging a large number of roots on the confocal microscope as part of a research project in my lab. I had already dabbled with Numbers for iPad, the native spreadsheet app by Apple, so I thought of it as a means to capture information about the particular root under observation. I created a new plain spreadsheet with a column for the file name, so I could match it up to the confocal image later. I was just planning to capture the file name and notes about that root, but then I noticed the “check box” field type on the soft keyboard that opens when editing a cell in Numbers. So I ended up including a couple of those true/false indicators for the observations, leaving the notes field for specific features of the root under observation. The image below represents my data table with a few observations populating it.

Table from Numbers for iPad

Data entry table in Numbers for iPad.

The first time I used Numbers like this, I just tapped on a cell to select it and begin editing and it was easy enough. Then I noticed the option to create a new form by clicking that “plus” tab above, and that lets you create a nice input form rather than poking a cell at a time.

Data entry form in Numbers for iPad

A data entry form in Numbers for iPad.

This streamlines the data entry process quite a bit, and actually treats the rows of the table as though they are individual records in a simple database. As far as I can tell, the form view is not editable, it just automatically populates based on the contents of the table to which it is linked. This keeps it simple, but ideally one would be able to exclude certain fields from a form like this and have them auto-complete (such as the date field). But still, this is the kind of simplification that really helps one to remain focused on the research rather than record-keeping while at the bench. Not having to scan an entire worksheet for the right cell to enter a value into is a big step forward, in other words.

I plan to keep working through examples of common work in the lab and whether that work is facilitated by the iPad or made needlessly more complex. In the case of the iPad for routine record-keeping, I like it so far. It’s like a fancy electronic clipboard with an endless supply of customized forms waiting to be created.

The BGI gets serious about sequencing

A special report on the human genome: The dragon’s DNA | The Economist

That contact will shortly be made with the delivery of 120 spanking new top-of-the-range Illumina sequencing machines. When they have all been installed the building will, so it is claimed, have more DNA-sequencing capacity than the whole of the United States. And that is just the start.